ensembl2geneinfo: Ensembl ids 2 hgnc and various info

In letaylor/bioutils: Useful functions for computational biology

Description

ensembl2geneinfo looks up information from var_attributes for Ensembl gene ids. If "hgnc_symbol" and "external_gene_name" in var_attributes, external_gene_name will not be returned but will be used to fill in blanks within hgnc_symbol.

Usage

ensembl2geneinfo(ensembl_gene_ids, host = "grch37.ensembl.org",
  var_attributes = c("ensembl_gene_id", "hgnc_symbol",
  "external_gene_name", "start_position", "end_position", "strand"),
  drop_dot_ensembl_id = TRUE)

Arguments

ensembl_gene_ids	Character vector. List of Ensembl gene ids to get hgnc symbols for.
host	Character. Ensembl biomaRt host.
var_attributes	Character vector. List of attributes to select from Ensembl.
drop_dot_ensembl_id	Logical. Drop "." from ENSG00000072310.12

Value

Data.frame. Data.frame of the attributes requested. Note that duplicates are removed and the order is not the same as given. First column is always ensembl_gene_ids_original.

Examples

ensembl2geneinfo(
    c("ENSG00000109501", "ENSG00000072310.12", "ENSG00000030066")
)

letaylor/bioutils documentation built on May 5, 2019, 7:09 a.m.